RESEARCH

GlyCORE Computational Chemistry and Bioinformatics Research CORE (CCBRC)

• Structures and properties of small molecules containing sugar moieties

• Structures and properties of glycoconjugates such as glycoproteins

• Protein-ligand interactions in which either the protein or ligand or both contain glyco groups

• Bioinformatics analysis of big data such as the outputs of mass spectrometry of glycoconjugate mixtures

• Other bioinformatics, such as for pathway analysis of glycosylation

Publications:

• GS Dasanayake; CM Hamadani; F Hailu; I Owolabi; M Patel; CM Chism; V Toragall; SK Misra; ME Jahan; SK Mishra; P Vashisth; JS Sharp; A Flynt; RJ Doerksen; TA Werfel; G Singh; EEL Tanner “Glyco ionic liquids as novel nanoparticle coatings to enhance triple-negative breast cancer drug delivery.” Accepted to Advanced Healthcare Materials (6/2025). doi: 10.1002/adhm.202500592 

• M Farrag; R Aljuhani; J Benicky; H Al Ahmed; SK Misra; SK Mishra; JS Sharp; RJ Doerksen; R Goldman; VH Pomin “Heparan-6-O-endosulfatase 2, a cancer-related proteoglycan enzyme, is effectively inhibited by a specific sea cucumber fucosylated glycosaminoglycan.” Glycobiology 35, cwaf025 (2025). doi: 10.1093/glycob/cwaf025   

• P Samanta; RJ Doerksen “Applying molecular modeling to predict novel FmlH-binding glycomimetics with improved pharmacokinetic properties for the prevention of urinary tract infections,” Applied Sciences 14, 9496 (2024). doi: 10.3390/app14209496 

• N Osada; SK Mishra; M Nakano; Y Tokoro; M Nagae; RJ Doerksen; Y Kizuka “Self-regulation of MGAT4A and MGAT4B activity toward glycoproteins through interaction of lectin domain with their own N-glycans,” iScience 27, 111066 (2024). doi: 10.1016/j.isci.2024.111066 

• P Samanta; RJ Doerksen “Identifying p56lck SH2 domain inhibitors using molecular docking and in silico scaffold hopping,” Applied Sciences 14, 4277 (2024). doi: 10.3390/app14104277 

• P Samanta; SK Mishra; VH Pomin; RJ Doerksen “Docking and molecular dynamics simulations clarify binding sites for interactions of novel marine sulfated glycans with SARS-CoV-2 spike glycoprotein,” Molecules 28, 6413 (2023). Special Issue on “New Insights into Biomolecular Structures and Interactions”. doi: 10.3390/molecules28176413 PMID: 37687244

• P Samanta; RJ Doerksen “Identifying FmlH lectin-binding small molecules for the prevention of Escherichia coli-induced urinary tract infections using hybrid fragment-based design and molecular docking,” Computers in Biology and Medicine 163, 107072 (2023). doi: 10.1016/j.compbiomed.2023.107072 PMID: 37329611

• AK Maurya; P Sharma; P Samanta; AA Shami; SK Misra; F Zhang; R Thara; D Kumar; D Shi; RJ Linhardt; JS Sharp; RJ Doerksen; R Tandon; VH Pomin “Structure, anti-SARS-CoV-2, and anticoagulant effects of two sulfated galactans from the red alga Botryocladia occidentalis,” International Journal of Biological Macromolecules 238, 124168 (2023). doi: 10.1016/j.ijbiomac.2023.124168 PMID: 36963552

• R Alkhodier; SK Mishra; RJ Doerksen; DA Colby “Comparison of conformational analyses of naturally occurring flavonoid-O-glycosides with unnatural flavonoid-CF2-glycosides using molecular modeling,” Journal of Chemical Information & Modeling 63, 375-386 (2023). doi: 10.1021/acs.jcim.2c01147 PMID: 36512328

• SB Kim; M Farrag; SK Mishra; SK Misra; JS Sharp; RJ Doerksen; VH Pomin “Selective 2-desulfation of tetrasaccharide-repeating sulfated fucans during oligosaccharide production by mild acid hydrolysis,” Carbohydrate Polymers 301A, 120316 (2023). doi: 10.1016/j.carbpol.2022.120316 PMID: 36436858 

• OT Shofolawe-Bakare; JU de Mel; SK Mishra; MA Hossain; CM Hamadani; MC Pride; GS Dasanayake; WA Monroe; EW Roth; EEL Tanner; RJ Doerksen; AE Smith; TA Werfel "ROS-responsive glycopolymeric nanoparticles for enhanced drug delivery to macrophages," Macromolecular Bioscience 22, 202200281 (2022). doi: 10.1002/mabi.202200281 PMID: 36125638

• M Nagae; T Hirata; H Tateno; SK Mishra; N Manbe; N Osada; Y Tokoro; Y Yamaguchi; RJ Doerksen; T Shimizu; Y Kizuka “Discovery of a lectin domain that regulated enzyme activity in N-acetylglucosaminyltransferase-IVa (MGAT4A),” Communications Biology 5, 695 (2022). doi: 10.1038/s42003-022-03661-w PMID: 35854001 

• SB Kim; M Zoepfl; P Samanta; F Zhang; K Xia; R Thara; RJ Linhardt; RJ Doerksen; MA McVoy; VH Pomin “Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties,” Journal of Biological Chemistry 298, 101856 (2022). doi: 10.1016/j.jbc.2022.101856 PMID:

• AM Vibhute; H-N Tanaka; SK Mishra; M Nagae; C Yonekawa; H Korekane; RJ Doerksen; H Ando; Y Kizuka “Structure-based design of UDP-GlcNAc analogs as candidate GnT-V inhibitors,” BBA General Subjects 1866(6): 130118 (2022). doi: 10.1016/j.bbagen.2022.130118 PMID: 35248671.

• R Dwivedi; P Samanta; P Sharma; F Zhang; SK Mishra; P Kucheryavy; SB Kim; AO Aderibigbe; RJ Linhardt; R Tandon; RJ Doerksen; VH Pomin “Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection,” Journal of Biological Chemistry 297, 101207 (2021). doi: 10.1016/j.jbc.2021.101207 PMID: 34537241

• VK Shankar; A Police; P Pandey; ZG Cuny; MA Repka; RJ Doerksen; SN Murthy “Optimization of sulfobutyl-ether-β-cyclodextrin levels in oral formulations to enhance progesterone bioavailability,” International Journal of Pharmaceutics 596, 120212 (2021). doi: 10.1016/j.ijpharm.2021.120212

• FF Bezerra; WP Vignovich; AO Aderibigbe; H Liu; J Sharp; RJ Doerksen; VH Pomin “Conformational properties of L-fucose and the tetrasaccharide building block of the sulfated L-fucan from Lytechinus variegatus,” Journal of Structural Biology 209, 107407 (2020). doi: 10.1016/j.jsb.2019.107407 PMID: 31698075

• Y Zou; X Wang; J Sims; B Wang; P Pandey; CL Welsh; RP Stone; MA Avery; RJ Doerksen; D Ferreira; C Anklin; FA Valeriote; M Kelly; MT Hamann “Computationally-assisted discovery and assignment of a highly strained and PANC-1 selective alkaloid from Alaska’s deep ocean,” Journal of the American Chemical Society 141, 4338-4344 (2019). doi: 10.1021/jacs.8b11403 PMID: 30758203 

• LG Malak; MA Ibrahim; AM Moharram; P Pandey; B Tekwani; RJ Doerksen; D Ferreira; SA Ross “Antileishmanial Carbasugars from Geosmithia langdonii,” Journal of Natural Products 81, 2222-2227 (2018). doi: 10.1021/acs.jnatprod.8b00473 PMID: 30298736

• NN Mohammed; P Pandey; KM Elokely; HL Liu; RJ Doerksen; MA Repka “Clotrimazole-cyclodextrin based approach for the management and treatment of Candidiasis. A formulation and chemistry based evaluation,” Pharmaceutical Development and Technology, 21, 619-629 (2016). doi: 10.3109/10837450.2015.1041041 PMID: 25923135

• MM Ghoneim; KM Elokely; AA El-Hela; AEI Mohammad; M Jacob; M Radwan; RJ Doeksen; SJ Cutler; SA Ross “Asphodosides A-E, anti-MRSA metabolites from Asphodelus microcarpus,” Phytochemistry, 105, 79-84 (2014). doi: 10.1016/j.phytochem.2014.06.011         

• MM Ghoneim, KM Elokely; AA El-Hela; AEI Mohammad; M Jacob; SJ Cutler; RJ Doerksen; SA Ross “Isolation and characterization of new secondary metabolites from Asphodelus microcarpus,” Medicinal Chemistry Research, 23, 3510-3515 (2014). doi: 10.1007/s00044-014-0928-x

• KM Elokely; RJ Doerksen “Docking challenge: Protein sampling and molecular docking performance,” Journal of Chemical Information & Modeling, 53, 1934–1945 (2013). doi: 10.1021/ci400040d PMID: 23530568 Featured on the cover of Issue 11, November 2013. Cited >150 times.

Through computational modeling of the requirements for modulating the cannabinoid (CB) receptor subtypes, CB1 and CB2, which are class-A G-protein coupled receptors (GPCRs), we intend to discover molecules which act through the CB receptors and that could later be developed into new drugs to treat many important human ailments including neuropathic pain, neuroinflammation, ischemic/reperfusion injury, anxiety, multiple sclerosis, and epilepsy. 

Publications:

• K Chaturvedi; KS Bledsoe; P Pandey; AG Osman; AG Chittiboyina; RJ Doerksen; M Godfrey “Prediction and assessment of energetically-favored binding orientation of cannabidiol at hNav1.1 channel using all-atom molecular dynamics simulations.” Journal of Biomolecular Structure & Dynamics, 1-10 (2025). doi: 10.1080/07391102.2025.2477778 PMID: 40105783 

• P Pandey; A Zagzoog; RB Laprairie; WM Neal; RJ Doerksen; AG Chittiboyina “Determination of the negative allosteric binding site of cannabidiol at the CB1 receptor: A combined computational and site-directed mutagenesis study.” ACS Chemical Neuroscience, 16, 311-328 (2025). doi: 10.1021/acschemneuro.4c00343 PMID: 39812521 

• MM Benjamin; GS Hanna; CF Dickinson; Y-M Choo; X Wang; J Downs-Bowen; R De; T McBrayer; RF Schinazi; SE Nielson; JM Hevel; P Pandey; RJ Doerksen; DM Townsend; J Zhang; Z Ye; S Wyer; L Bialousow; MT Hamann “Cannabinoid-inspired inhibitors of the SARS-CoV-2 coronavirus 2′-O-methyltransferase (2′-O-MTase) non-structural protein (Nsp10–16)”. Molecules, 29, 5081. Special Issue “Naturally Inspired Molecules as Inhibitors in Drug Discovery”. doi: 10.3390/molecules29215081 PMID: 39519722 

• K Chaturvedi; CS Anthony; P Pandey; RJ Doerksen; M Godfrey “Influence of structural characteristics on the binding of synthetic cannabinoids from the JWH family to the CB1 receptor: A computational study,” Journal of Molecular Graphics and Modeling 126, 108620 (2023). doi: 10.1016/j.jmgm.2023.108620 PMID: 37722351 

• A Police; VK Shankar; P Pandey; S Rangappa; RJ Doerksen; SN Murthy “Novel topical anandamide formulation for alleviating peripheral neuropathic pain,” International Journal of Pharmaceutics 641, 123085 (2023). doi: 10.1016/j.ijpharm.2023.123085 PMID: 37245739 

• P Pandey; M Kumarihamy; K Chaturvedi; MA Ibrahim; JA Lambert; M Godfrey; RJ Doerksen; I Muhammad “In vitro and in silico studies of neolignans from Magnolia grandiflora L. seeds against human cannabinoids and opioid receptors,” Molecules 28, 1253 (2023). Special issue on “New Insights into Biomolecular Structures and Interactions.” doi: 10.3390/molecules28031253 PMID: 36770918

• AH Tarawneh; P Pandey; LA Al-Momani; AV Gadetskaya; ST Abu-Orabie; RJ Doerksen; SJ Cutler “1,2,3-Triazole derivatives as highly selective cannabinoid receptor type 2 (CB2) agonists,” Arabian Journal of Chemistry 15, 103545 (2022). doi: 10.1016/j.arabjc.2021.103545 

• AO Aderibigbe; P Pandey; RJ Doerksen “Negative allosteric modulators of cannabinoid receptor 1: Modeling of ORG27569 interactions on CB1 bound to CP55940 in light of recent X-ray structures,” Journal of Biomolecular Structure and Dynamics 40, 5729-5747 (2022). doi: 10.1080/07391102.2021.1873187 PMID: 33480332

• P Pandey; KK Roy; RJ Doerksen “Negative allosteric modulators of cannabinoid receptor 2: Protein modeling, binding site identification and molecular dynamics simulations in the presence of an orthosteric agonist,” Journal of Biomolecular Structure and Dynamics 38, 32-47 (2020). doi: 10.1080/07391102.2019.1567384 PMID: 30652534.

• P Pandey; KK Roy; H Liu; G Ma; SA Pettaway; WF Alsharif; RS Gadepalli; JM Rimoldi; CR McCurdy; SJ Cutler; RJ Doerksen “Structure-based identification of potent natural product chemotypes as cannabinoid receptor 1 inverse agonists,” Molecules 23, 2630 (2018). Invited. Special issue on “Hit Generation and Verification for Novel Lead Compounds.” doi: http://10.3390/molecules23102630 PMID:

• J Pressly; SM Mustafa; AH Abidi; S Alghamdi; P Pandey; KK Roy; RJ Doerksen; BM Moore; F Park “Selective cannabinoid 2 receptor stimulation reduces tubular epithelial cell damage following renal ischemia-reperfusion injury,” Journal of Pharmacology and Experimental Therapeutics, 364, 287-299 (2018). doi: http://10.1124/jpet.117.245522 PMID: 29187590 PMCID: PMC5774215

• H Liu; RY Patel; RJ Doerksen “Structure of the cannabinoid receptor 1: Homology modeling of the inactive state and enrichment study based on CB1 antagonist docking.” MedChemComm, 5, 1297-1302 (2014). doi: 10.1039/C4MD00121D Inside cover article.

• S Liu; RY Patel; PR Daga; H Liu; G Fu; RJ Doerksen; Y Chen; D Wilkins “Combined rule extraction and feature elimination in supervised classification,” IEEE Transactions on Nanobioscience, 11, 228-236 (2012). doi: 10.1109/TNB.2012.2213264; PMID: 22987128

• LK Brents; F Medina-Bolivar; KA Seely; V Nair; SM Bratton; A Gallus-Zawada; L Ñopo; RY Patel; H Liu; RJ Doerksen; PL Prather; A Radominska-Pandya “Natural prenylated resveratrol analogs arachidin-1 and -3 demonstrate improved glucuronidation profiles and have affinity for cannabinoid receptors,” Xenobiotica, 42, 139-156 (2012). doi: 10.3109/00498254.2011.609570

Past Funding:

• National Institutes of Health. National Institute of General Medical Sciences Award Number P30GM122733. (PI: Dr. Soumyajit Majumdar) Center of Biomedical Research Excellence – Natural Products Neuroscience (COBRE-NPN). Total budget ~$5,373,000. Voucher Program Award, “Assays to aid in the discovery of novel CB1 antagonists void of adverse neuropsychiatric effects." Robert J. Doerksen, Principal Investigator. 3/10/2020-5/31/2020. $4794 value. 

• National Science Foundation. XSEDE (Extreme Science and Engineering Discovery Environment) Startup request. “Molecular dynamics simulations to understand the conformational changes of the CB1–THC–CBD–5-HT2A heteromer: Molecular mechanism of CBD binding.” CHE190092. 10/23/2019-10/22/2020; extended to 4/22/2021. Robert J. Doerksen, Co-Investigator (Amar Chittaboyina, PI). Award amount: $1,932.61 (estimated value). 

• National Science Foundation. XSEDE (Extreme Science and Engineering Discovery Environment) Startup request. “Extended all-atom molecular dynamics simulations to shed light on the characteristic features from inactive- to active-state transition of the human CB2 receptor, energetically preferred binding pose recognition, and agonist-induced conformational changes during receptor activation.” MCB190035. 4/15/2019-4/14/2020. Robert J. Doerksen, Co-Investigator (Pankaj Pandey, PI). Award amount: $1,932.61 (estimated value) 

• National Science Foundation. XSEDE (Extreme Science and Engineering Discovery Environment) Startup request. “Computational modeling and dynamics studies of negative allosteric modulators within the orthosteric ligand–bound complexes of the human cannabinoid 1 (CB1) receptor.” MCB190033. 4/3/2019-4/2/2020. Robert J. Doerksen, Principal Investigator. Award amount: $1,748.75 (estimated value) 

• National Institutes of Health. R15. “Computer-aided Design and In vitro Testing of Novel Cannabinoid Receptor Modulators.” 5/1/2016-4/30/2019. Robert J. Doerksen, Principal Investigator.

• National Institutes of Health. National Institute of General Medical Sciences Award Number P30GM122733. (PI: Dr. Soumyajit Majumdar) Center of Biomedical Research Excellence – Natural Products Neuroscience (COBRE-NPN) Voucher Program Award, "Computer-aided discovery of CB1 antagonists void of adverse neuropsychiatric effects." Robert J. Doerksen, Principal Investigator. 3/5/2019-5/31/2019. $1248 

• University of Mississippi’s National Institutes of Health (NIH) National Center for Research Resources (NCRR) Center of Research Excellence in Natural Products Neuroscience (CORE-NPN) Phase II. “CORE-NPN: Rational Design of Novel Natural Product-Derived Cannabinoid Ligands.” P20GM104932. 9/1/2015-8/31/2016. Robert J. Doerksen, Chemistry Core Participant (PI: Dr. Stephen J. Cutler, University of Mississippi.) Funding for 3 months of postdoctoral fellow support.

• University of Mississippi’s National Institutes of Health (NIH) National Center for Research Resources (NCRR) Center of Research Excellence in Natural Products Neuroscience (CORE-NPN) Phase II. “CORE-NPN: Rational Design of Novel Natural Product-Derived Cannabinoid Ligands.” P20GM104932. Robert J. Doerksen, Junior Investigator. (PI: Dr. Stephen J. Cutler, University of Mississippi.) 7/1/2012-8/31/2015.

• Extreme Science and Engineering Discovery Environment (XSEDE) grant of supercomputer time, MCB140248 “Computational insights into the characteristic features of the active state 3D structure of the human CB2 receptor, mode of agonist recognition and agonist-induced conformational changes during receptor activation.” Robert J. Doerksen, Co-Investigator. (PI: Dr. Kuldeep K. Roy, postdoctoral fellow) 9/2014-11/2015.

• University of Mississippi’s National Institutes of Health (NIH) National Center for Research Resources (NCRR) Center of Research Excellence in Natural Products Neuroscience (CORE-NPN) Junior Investigator Program. “CORE-NPN: Rational Design of Novel Natural Product-Derived Cannabinoid Ligands.” Robert J. Doerksen, Principal Investigator. (PI: Dr. Stephen J. Cutler, University of Mississippi.) 7/1/2009-6/30/2011.

• National Science Foundation. Mississippi EPSCoR Program. Targeted Seed Grant. “Combined Computational Chemistry and Computational Biology Modeling for Understanding Protein-Protein and Protein-Ligand Interactions.” 1/1/2011-12/31/2011. Robert J. Doerksen, Principal Investigator.

Nature is an excellent source of diverse molecules with intriguing properties. Such molecules are being discovered, characterized and tested as potential drug leads for a wide range of human health targets. In collaborative projects with natural product chemists and biologists, my research group performs calculations of the electronic structure of molecules to study their conformational flexibility and to help assign their conformation and absolute configuration. We also study the interactions of the molecules with protein targets to help elucidate their mechanism of bioactivity. 

Publications:

• P Pandey; M Kumarihamy; K Chaturvedi; MA Ibrahim; JA Lambert; M Godfrey; RJ Doerksen; I Muhammad “In vitro and in silico studies of neolignans from Magnolia grandiflora L. seeds against human cannabinoids and opioid receptors,” Molecules 28, 1253 (2023). Special issue on “New insights into biomolecular structures and interactions.” doi: 10.3390/molecules28031253 PMID: 36770918 

• Y Liu; P Gao; X Liang; Y Zhang; X Yu; X Xue; L Kockaya; P Pandey; RJ Doerksen; X Wang; G Yao; W Chu; X Chen; S Song; MT Hamann; L Li “Prenylated flavonoids with significant anti-hepatoma activity from Daphne giraldii and effects on Fibroblast Growth Factor Receptor 1 (FGFR1),” European Journal of Medicinal Chemistry 247, 115006 (2023). doi: 10.1016/j.ejmech.2022.115006 PMID: 36549116

• ND Chaurasiya; J Midiwo; P Pandey; RJ Doerksen; I Muhammad; BL Tekwani “Selective interactions of O-methylated flavonoid natural products with human monoamine oxidase-A and -B,” Molecules 25, 5358 (2020). Special issue in honor of Prof. James D. McChesney on the occasion of his 80th birthday. doi: 10.3390/molecules25225358 PMID: 33212830 

• SK Tripathi; Q Feng; L Liu; DE Levin; KK Roy; RJ Doerksen; SR Baerson; X Shi; X Pan; W-H Xu; X-C Li; AM Clark; AK Agarwal “Puupehenone, a marine sponge-derived sesquiterpene quinone, potentiates the antifungal drug caspofungin by disrupting Hsp90 activity and the cell wall integrity pathway,” mSphere 5, e00818-19 (2020). Editor’s Pick. doi: 10.1128/mSphere.00818-19 PMID: 31915228 

• J Liu; P Pandey; X Wang; K Adams; X Qi; J Chen; H Sun; Q Hou; D Ferreira; RJ Doerksen; MT Hamann; S Li “Hepatoprotective tetrahydrobenzocyclooctabenzofuranone lignans from Kadsura longipedunculata,” Journal of Natural Products 82, 2842-2851 (2019). doi: 10.1021/acs.jnatprod.9b00576 PMID: 31556297 

• Y Zou; X Wang; J Sims; B Wang; P Pandey; CL Welsh; RP Stone; MA Avery; RJ Doerksen; D Ferreira; C Anklin; FA Valeriote; M Kelly; MT Hamann “Computationally-assisted discovery and assignment of a highly strained and PANC-1 selective alkaloid from Alaska’s deep ocean,” Journal of the American Chemical Society 141, 4338-4344 (2019). doi: 10.1021/jacs.8b11403 PMID: 30758203 

• LG Malak; MA Ibrahim; AM Moharram; P Pandey; B Tekwani; RJ Doerksen; D Ferreira; SA Ross “Antileishmanial carbasugars from Geosmithia langdonii,” Journal of Natural Products 81, 2222-2227 (2018). doi: http://10.1021/acs.jnatprod.8b00473

• X Wang; J Liu; P Pandey; FR Fronczek; RJ Doerksen; J Chen; X Qi; P Zhang; D Ferreira; FA Valeriote; H Sun; S Li; MT Hamann “Computationally assisted assignment of the kadsuraols, a class of chemopreventive agents for the control of liver cancer,” Organic Letters 20, 5559–5563 (2018). doi: http://10.1021/acs.orglett.8b02207

• J Liu; P Pandey; X Wang; X Qi; J Chen; H Sun; P Zhang; Y Ding; D Ferreira; RJ Doerksen; MT Hamann; S Li “Hepatoprotective dibenzocyclooctadiene and tetrahydrobenzocyclooctabenzofuranone lignans from Kadsura longipedunculata,” Journal of Natural Products 81, 846-857 (2018). doi: http://10.1021/acs.jnatprod.7b00934

• X Wang; J Liu; P Pandey; J Chen; FR Fronczek; S Parnham; X Qi; RJ Doerksen; D Ferreira; H Sun; S Li; MT Hamann “Assignment of the absolute configuration of hepatoprotective highly oxygenated triterpenoids using X-ray, ECD, NMR J-based configurational analysis and HSQC overlay experiments,” BBA (Biochimica et Biophysica Acta) General Subjects, 1861, 3089-3095 (2017). doi: http://10.1016/j.bbagen.2017.09.001 PMID: 28919469

• J Oh; H Liu; HB Park; D Ferreira; G-S Jeong; MT Hamann; RJ Doerksen; MK Na “In silico investigation of lavandulyl flavonoids for the 2 development of potent FAS-inhibitory prototypes,” BBA (Biochimica et Biophysica Acta) General Subjects, 1861, 3180-3188 (2017). doi: 10.1016/j.bbagen.2016.08.001 PMID: 27531709

• AD Priyanto; RJ Doerksen; C-I Chang; Y-C Lin; T-C Wang; SB Widjanarko; J Kusnadi; J-L Hsu “Screening, discovery, and characterization of angiotensin-I converting enzyme inhibitory peptides derived from proteolytic hydrolysate of bitter melon seed proteins,” Journal of Proteomics, 128, 424-435 (2015). doi: 10.1016/j.jprot.2015.08.018

• AD Priyanto; RJ Doerksen; C-I Chang; Y-C Lin; T-C Wang; SB Widjanarko; J Kusnadi; J-L Hsu “Data in support of optimized production of angiotensin-I converting enzyme inhibitory peptides derived from proteolytic hydrolysate of bitter melon seed proteins,” Data in Brief, 5, 403-407 (2015). doi: 10.1016/j.dib.2015.09.038

• P-S Su; RJ Doerksen; S-H Chen; W-C Sung; RDS Rawendra; C-R Chen; J-W Li; Aisha; T-C Huang; C-I Chang; M-H Liao; J-L Hsu “Screening and profiling stilbene-type natural products with angiotensin-converting enzyme inhibitory activity from Ampelopsis brevipedunculata var. hancei (Planch.) Rehder,” Journal of Pharmaceutical and Biomedical Analysis, 108, 70-77 (2015). doi: 10.1016/j.jpba.2015.01.053

• MM Ghoneim; KM Elokely; AA El-Hela; AEI Mohammad; M Jacob; M Radwan; RJ Doeksen; SJ Cutler; SA Ross “Asphodosides A-E, anti-MRSA metabolites from Asphodelus microcarpus,” Phytochemistry, 105, 79-84 (2014). doi: 10.1016/j.phytochem.2014.06.011

• MM Ghoneim, KM Elokely; AA El-Hela; AEI Mohammad; M Jacob; SJ Cutler; RJ Doerksen; SA Ross “Isolation and characterization of new secondary metabolites from Asphodelus microcarpus,” Medicinal Chemistry Research, 23, 3510-3515 (2014). doi: 10.1007/s00044-014-0928-x

• MAM Ibrahim; M Na; J Oh; RF Schinazi; TR McBrayer; T Whitaker; RJ Doerksen; DJ Newman; LG Zachos; MT Hamann “The significance of endangered and threatened plant natural products in the control of human disease,” Proceedings of the National Academy of Sciences of the United States of America, 110, 16832-16837 (2013). doi: 10.1073/pnas.1311528110 Featured article in University of Washington’s Conservation Magazine and “Featured article recommended for teaching” in “F1000Prime”.

• IH Hwang; J Oh; A Kochanowska-Karamyan; RJ Doerksen; M Na; MT Hamann “A novel natural phenyl alkene with cytotoxic activity,” Tetrahedron Letters, 54, 3872-3876 (2013). doi: 10.1016/j.tetlet.2013.05.032

• J Oh; JJ Bowling; Y Zou; AG Chittiboyina; RJ Doerksen; D Ferreira; TD Leininger; MT Hamann “Configurational assignments of conformationally restricted bis-monoterpene hydroquinones: Utility in exploration of endangered plants,” Biochemica et Biophysica Acta (BBA) – General Subjects, 1830, 4229-4234 (2013). doi: 10.1016/j.bbagen.2013.04.029; PMID: 23628705

• MA Albadry; KM Elokely; B Wang; JJ Bowling; MF Abdelwahab; MH Hossein; RJ Doerksen; MT Hamann “Computationally assisted assignment of Kahalalide Y configuration using an NMR-constrained conformational search,” Journal of Natural Products, 76, 178-185 (2013). doi: 10.1021/np3006088; PMID: 23363083

• H Liu; A Dasmahapatra; RJ Doerksen “Computational study on the conformations of gambogic acid,” Chemical Physics Letters, 511, 405-412 (2011). doi: 10.1016/j.cplett.2011.06.035; PMID: 22991483

• R Mohammed; J Peng; M Kelly; M Yousaf; E Winn; S Odde; Z Bie; A Xie; RJ Doerksen; MT Hamann “Polyketide-peroxides from a species of Jamaican plakortis (Porifera: Demospongiae),” Australian Journal of Chemistry, 63, 1-9 (2010). Special Issue. doi: 10.1071/CH09665

• H Liu; CR McCurdy; RJ Doerksen “Computational study on the conformations of mitragynine and mitragynaline,” Journal of Molecular Structure: Theochem, 945, 57-63 (2010). doi: 10.1016/j.theochem.2010.01.011; PMID: 21293786

• J Peng; S Kudrimoti; S Prasanna; S Odde; RJ Doerksen; HK Pennaka; Y-M Choo; KV Rao; BL Tekwani; V Madgula; SI Khan; B Wang; AMS Mayer; MR Jacob; LC Tu; J Gertsch; MT Hamann “Structure activity relationship and mechanism of action studies of manzamine analogues for the control of neuroinflammation and cerebral infections,” Journal of Medicinal Chemistry, 53, 61-76 (2010). doi: 10.1021/jm900672t; PMID: 20017491 Cited >35 times.

• S Kudrimoti; SA Ahmed; PR Daga; AE Wahba; SI Khalifa; RJ Doerksen; MT Hamann “Semisynthetic latrunculin B analogs: Studies of actin docking support a proposed mechanism for latrunculin bioactivity,” Bioorganic & Medicinal Chemistry, 17, 7517-7522 (2009). doi: 10.1016/j.bmc.2009.09.012; PMID: 19800245

• MA Ibrahim; AG Shilabin; S Prasanna; M Jacob; SI Khan; RJ Doerksen; MT Hamann “2-N-Methyl modifications and SAR studies of manzamine A,” Bioorganic & Medicinal Chemistry, 16, 6702-6706 (2008). PMID: 18595720

• SA Ahmed; S Odde; PR Daga; JJ Bowling; MK Mesbah; DT Youssef; SI Khalifa; RJ Doerksen; MT Hamann “Latrunculin with a highly oxidized thiazolidinone ring:  Structure assignment and actin docking,” Organic Letters 9, 4773-4776 (2007). doi: 10.1021/ol7020675 Cited >21 times.

Current Funding:

• National Science Foundation. Research Experience for Undergraduates (REU). “Ole Miss Physical Chemistry Summer Research Program REU.” Second Competitive Renewal. CHE1757888. Robert J. Doerksen, Senior Personnel. (PI: Dr. Nathan Hammer, U. Mississippi.) 9/1/2018-8/31/2021. COVID extension to 8/31/2022. Total budget $299,682. Doerksen research group has one summer student each summer. 

Past Funding:

• National Science Foundation. Research Experience for Undergraduates (REU). “Ole Miss Physical Chemistry Summer Research Program REU.” CHE-1460568. (Renewal) 9/1/2015-8/31/2018. Robert J. Doerksen, Senior Personnel. (PI: Dr. Nathan Hammer, Department of Chemistry, University of Mississippi.) $326,697. Doerksen research group had one summer student each summer.

The tuberculosis research listed here represents the results of an ongoing collaboration with Prof. Sudeshna Roy of U. Tennessee Health Sciences Center and others.

Preprint:

• S Roy; T Berida; T-Y Huang; SC Weck; M Lutz; SR McKee; N Kagerah; DL Manning; ME Jahan; SK Mishra; RJ Doerksen; CL Stallings; C Ducho “1,2,4-Triazole-based first-in-class non-nucleoside inhibitors of bacterial enzyme MraY.” bioRxiv 2025.01.30.635793; doi: https://doi.org/10.1101/2025.01.30.635793 

Publications:

• T Berida; SR McKee; S Chatterjee; D Manning; W Li; P Pandey; SK Tripathi; Y Mreyoud; A Smirnov; RJ Doerksen; M Jackson; C Ducho; CL Stallings; S Roy “Discovery, synthesis, and optimization of 1,2,4-triazolyl pyridines targeting Mycobacterium tuberculosis,” ACS Infectious Diseases 9, 2282-2298 (2023). doi: 10.1021/acsinfecdis.3c00341 PMID: 37788674 

• P Pandey; S Chatterjee; T Berida; RJ Doerksen; S Roy “Identification of potential non-nucleoside MraY inhibitors for tuberculosis chemotherapy using structure-based virtual screening,” Journal of Biomolecular Structure and Dynamics 40, 4832-4849 (2022). doi: 10.1080/07391102.2020.1862705 PMID: 33353500 

Patent:

• S Roy; RJ Doerksen; T Berida; C Stallings; S McKee; C Ducho “Selective agents targeting mycobacterium tuberculosis.” US Provisional Patent Application, Serial No. 63/267,357; Filing Date: Jan 2023, WO2023147571A3.

Past Funding:

• R21. AI142210. “Target-based chemotherapeutics development against Mycobacterium tuberculosis.” Robert J. Doerksen, Co-I. (PI: Dr. Sudeshna Roy, Division of Medicinal Chemistry). 7/1/2019-6/30/2021. No cost extension to 6/30/2022. Total budget: $411,092. 

We are interested to develop and test new methods for handling the enormous volumes of chemical information in order to find patterns and to build predictive models. For some of our work, we collaborated with research groups in UM’s Department of Computer & Information Science and Department of Biological Science.

Publications:

• G Fu; S Liu; X Nan; OR Dale; Z Zhao; Y Chen; DE Wilkins; SP Manly; SJ Cutler; RJ Doerksen “Quantitative structure-activity relationship analysis and a combined ligand-based/structure-based virtual screening study for glycogen synthase kinase-3.” Molecular Informatics, 33, 627–640 (2014). doi: 10.1002/minf.201400045

• Z Zhao; G Fu; S Liu; KM Elokely; RJ Doerksen; Y Chen; DE Wilkins “Drug activity prediction using multiple-instance learning via joint instance and feature selection,” BMC Bioinformatics, 14 (Suppl 14), S16 (12 pp) (2013). (2013 MCBIOS Proceedings). doi: 10.1186/1471-2105-14-S14-S16

• A Shayanfar; S Ghasemi; S Soltani; K Asadpour-Zeynali; RJ Doerksen; A Jouyban “Quantitative structure-activity relationships of imidazole-containing farnesyltransferase inhibitors using different chemometric methods,” Medicinal Chemistry, 9, 434-448 (2013). doi: 10.2174/1573406411309030014

• G Fu; X Nan; H Liu; RY Patel; PR Daga; Y Chen; DE Wilkins; RJ Doerksen “Implementation of multiple-instance learning in drug activity prediction,” BMC Bioinformatics, 13, (Suppl 15) S3 (2012). doi: 10.1186/1471-2105-13-S15-S3; PMID: 23046442 (2012 MCBIOS Proceedings).

• S Liu; RY Patel; PR Daga; H Liu; G Fu; RJ Doerksen; Y Chen; D Wilkins “Combined rule extraction and feature elimination in supervised classification,” IEEE Transactions on Nanobioscience, 11, 228-236 (2012). doi: 10.1109/TNB.2012.2213264; PMID: 22987128

• X Nan; G Fu; Z Zhao; S Liu; RY Patel; H Liu; PR Daga; RJ Doerksen; X Dang; Y Chen; D Wilkins “Leveraging domain information to restructure biological prediction.” BMC Bioinformatics, 12, S22 (15 pp.) (2011) (2011 MCBIOS Proceedings). doi: 10.1186/1471-2105-12-S10-S22; PMID: 22166097

• S Prasanna; RJ Doerksen “Topological polar surface area: A useful descriptor in 2D-QSAR,” Current Medicinal Chemistry, 16, 21-41 (2009). doi: 10.2174/092986709787002817 PMID: 19149561

Current Funding:

• National Institutes of Health. National Institute of General Medical Sciences. P20. GM130460. (Multi-PIs: Dr. Joshua Sharp, Division of Pharmacology and Dr. Samir Ross, National Center for Natural Products Research and Division of Pharmacognosy). “GlyCORE: Glycoscience Center of Research Excellence.” 5/15/2020-3/31/2025. $10,639,190. Doerksen is PI of the Computational Chemistry and Bioinformatics Research Center of Biomedical Research Excellence, with a total budget of $1,000,072.

Past Funding:

• National Science Foundation. Mississippi EPSCoR Program. Targeted Seed Grant. NSF EPS 0903787. “Combined Computational Chemistry and Computational Biology Modeling for Understanding Protein-Protein and Protein-Ligand Interactions.” 8/16/2015-8/15/2016. Robert J. Doerksen, Principal Investigator

• National Science Foundation. Mississippi EPSCoR Program “Modeling and Simulation of Complex Systems.” NSF EPS 0903787 and NSF EPS 1006883. 8/2009-8/2016. Robert J. Doerksen, Co-Investigator. (PI: Dr. Sandra Harpole, Mississippi State University.)

• National Science Foundation. Mississippi EPSCoR Program. Targeted Seed Grant. “Combined Computational Chemistry and Computational Biology Modeling for Understanding Protein-Protein and Protein-Ligand Interactions.” 1/1/2011-12/31/2011. 

We work with collaborators in UM’s Department of Pharmaceutics and Drug Delivery, Department of Bioengineering and Department of Chemistry and Biochemistry to find novel designs and practical methods for delivery of drugs, such as to kill cancer cells with minimized side effects on healthy cells. We perform an assortment of computations, such as on docking of nanoparticles to proteins and binding modes and energetics for interactions of drug molecules and cyclodextrins. 

Publications:

• A Police; VK Shankar; P Pandey; S Rangappa; RJ Doerksen; SN Murthy “Novel topical anandamide formulation for alleviating peripheral neuropathic pain,” International Journal of Pharmaceutics 641, 123085 (2023). doi: 10.1016/j.ijpharm.2023.123085 PMID: 37245739 

• OT Shofolawe-Bakare; JU de Mel; SK Mishra; MA Hossain; CM Hamadani; MC Pride; GS Dasanayake; WA Monroe; EW Roth; EEL Tanner; RJ Doerksen; AE Smith; TA Werfel "ROS-responsive glycopolymeric nanoparticles for enhanced drug delivery to macrophages," Macromolecular Bioscience 22, 202200281 (2022). doi: 10.1002/mabi.202200281 PMID: 36125638 

• VK Shankar; A Police; P Pandey; ZG Cuny; MA Repka; RJ Doerksen; SN Murthy “Optimization of sulfobutyl-ether-β-cyclodextrin levels in oral formulations to enhance progesterone bioavailability,” International Journal of Pharmaceutics 596, 120212 (2021). doi: 10.1016/j.ijpharm.2021.120212 PMID: 33493605 

• NN Mohammed; P Pandey; KM Elokely; HL Liu; RJ Doerksen; MA Repka “Clotrimazole-cyclodextrin based approach for the management and treatment of Candidiasis. A formulation and chemistry based evaluation,” Pharmaceutical Development and Technology, 21, 619-629 (2016). doi: 10.3109/10837450.2015.1041041

• J Bae; MA Nael; L Jiang; PT Hwang; F Mahdi; H-W Jun; WM Elshamy; Y-D Zhou; SN Murthy; RJ Doerksen; S Jo “Quinone propionic acid-based redox-triggered polymer nanoparticles for drug delivery: Computational analysis and in vitro evaluation,” Journal of Applied Polymer Science, 131 (2014). doi: 10.1002/app.40461

Past Funding:

• National Science Foundation. Mississippi EPSCoR Program. Year 4 Seed Grant. “Computational modeling-aided design, synthesis and optimization of redox-sensitive polymer nanoparticles with optimal colloid-forming and DT-diaphorase-substrate properties.” Robert J. Doerksen, Co-Investigator. (PI: Dr. Seongbong Jo, University of Mississippi.) 9/1/2012-8/31/2013.

• National Science Foundation. Mississippi EPSCoR Program. Year 3 Seed Grant. “Computational modeling-aided design, synthesis and evaluation of redox-sensitive polymer nanoparticles for cancer targeted drug delivery.” Robert J. Doerksen, Co-Investigator. (PI: Dr. Seongbong Jo, University of Mississippi.) 9/1/2011-8/31/2012. 

There is an urgent need for new antimalarial drugs, in part because the protozoa that cause the disease rapidly evolve resistance to drugs. We were also involved in study of the mechanism of action for the antimalarial effect and for side effects of the existing antimalarials, especially of the 8-aminoquinoline drugs which are the mainstay for liver-stage malaria. 

Publications:

• GC Brandão; FCR Missias; LM Arantes; LF Soares; KK Roy; RJ Doerksen; A Braga de Oliveira; GR Pereira “Antimalarial naphthoquinones. Synthesis via click chemistry, in vitro activity, docking to PfDHODH and SAR of lapachol-based compounds,” European Journal of Medicinal Chemistry, 145, 191-205 (2018). doi: http://10.1016/j.ejmech.2017.12.051 PMID: 29324340

• Y Ding; H Liu; BL Tekwani; NPD Nanayakkara; IA Khan; LA Walker; RJ Doerksen “Methemoglobinemia hemotoxicity of some antimalarial 8-aminoquinoline analogues and their hydroxylated derivatives: Density functional theory computation of ionization potentials,” Chemical Research in Toxicology, 29, 1132-1141 (2016). doi: 10.1021/acs.chemrestox.6b00063

• H Liu; Y Ding; LA Walker; RJ Doerksen “Computational study on the effect of exocyclic substituents on the ionization potential of primaquine: Insights into the design of primaquine-based antimalarial drugs with less methemoglobin generation,” Chemical Research in Toxicology, 28, 169-174 (2015). doi: 10.1021/tx500230t PMID: 25222923

• Y Ding; H Liu; NPD Nanayakkara; IA Khan; BL Tekwani; LA Walker; RJ Doerksen “Hydroxylated derivatives of NPC1161: Theoretical insights into their potential toxicity and the feasibility and regioselectivity of their formation,” Journal of Physical Chemistry A, 118, 5501–5507 (2014). doi: 10.1021/jp502612t

• H Liu; BL Tekwani; NPD Nanayakkara; LA Walker; RJ Doerksen “Methemoglobin generation by 8-aminoquinolines: Effect of substitution at 5-position of primaquine,” Chemical Research in Toxicology, 26, 1801-1809 (2013). doi: 10.1021/tx400067a

• H Liu; Y Ding; LA Walker; RJ Doerksen “Effect of antimalarial drug primaquine and its derivatives on the ionization potential of hemoglobin: A QM/MM study,” MedChemComm, 4, 1145-1147 (2013). doi: 10.1039/C3MD00045A Cover article, August 2013.

• A Shayanfar; S Ghasemi; S Soltani; K Asadpour-Zeynali; RJ Doerksen; A Jouyban “Quantitative structure-activity relationships of imidazole-containing farnesyltransferase inhibitors using different chemometric methods,” Medicinal Chemistry, 9, 434-448 (2013). doi: 10.2174/1573406411309030014

• H Liu; LA Walker; RJ Doerksen “DFT study on the radical anions formed by primaquine and its derivatives,” Chemical Research in Toxicology, 24, 1476-1485 (2011). doi: 10.1021/tx200094v; PMID: 21699254

• H Liu; LA Walker; NPD Nanayakkara; RJ Doerksen “Methemoglobinemia caused by 8-aminoquinoline drugs: DFT calculations suggest an analogy to H4B’s role in nitric oxide synthase,” Journal of the American Chemical Society, 133, 1172-1175 (2011). doi: 10.1021/ja107472c; PMID: 21244096

• J Peng; S Kudrimoti; S Prasanna; S Odde; RJ Doerksen; HK Pennaka; Y-M Choo; KV Rao; BL Tekwani; V Madgula; SI Khan; B Wang; AMS Mayer; MR Jacob; LC Tu; J Gertsch; MT Hamann “Structure activity relationship and mechanism of action studies of manzamine analogues for the control of neuroinflammation and cerebral infections,” Journal of Medicinal Chemistry, 53, 61-76 (2010). doi: 10.1021/jm900672t; PMID: 20017491

• P Sivaprakasam; PN Tosso; RJ Doerksen “Structure-activity relationship and comparative docking studies for cycloguanil analogs as PfDHFR-TS inhibitors,” Journal of Chemical Information & Modeling, 49, 1787-1796 (2009). doi: 10.1021/ci9000663; PMID: 19588935

• A Xie; S Odde; P Sivaprakasam; RJ Doerksen “Imidazole-containing farnesyltransferase inhibitors: 3D quantitative structure-activity relationship and molecular docking studies,” Journal of Computer-Aided Molecular Design, 23, 431-448 (2009). doi: 10.1007/s10822-009-9278-z; PMID: 19479325

• A Xie; SR Clark; S Prasanna; RJ Doerksen “3D quantitative structure-farnesyltransferase inhibition analysis for some diaminobenzophenones,” Journal of Enzyme Inhibition & Medicinal Chemistry, 24, 1220-1228 (2009). doi: 10.3109/14756360902781389; PMID: 19912055

• MA Ibrahim; AG Shilabin; S Prasanna; M Jacob; SI Khan; RJ Doerksen; MT Hamann “2-N-Methyl modifications and SAR studies of manzamine A,” Bioorganic & Medicinal Chemistry, 16, 6702-6706 (2008). PMID: 18595720

• A Xie; P Sivaprakasam; RJ Doerksen “3D-QSAR analysis of antimalarial farnesyltransferase inhibitors based on a 2, 5-diaminobenzophenone scaffold,” Bioorganic & Medicinal Chemistry 14, 7311-7323 (2006). doi: 10.1016/j.bmc.2006.06.041; PMID: 16837204 

Past Funding:

• USAID (American Council on Education/US Agency for International Development). “Africa-U.S. Network of Centers of Excellence in Water & Environmental Science & Technology.” AEG-A-00-05-00007. Robert J. Doerksen, Co-Investigator. (PI: Dr. Nosa Egiebor, University of Mississippi.) 8/1/2014-6/30/2015

• Department of Defense USAMRMC. “Development of Safer Antimalarial and Antileishmanial Drugs for US Troops and Travelers.” Robert J. Doerksen, Investigator. (PI: Dr. Larry Walker, University of Mississippi.) 9/2009-12/2012

• Centers for Disease Control and Prevention (CDC) National Center for Zoonotic, Vector-Borne, and Enteric Diseases (NCZVED). “Development and Testing of New Antimalarial Drugs.” Robert J. Doerksen, Investigator. (Dr. Mitchell Avery, PI, University of Mississippi.) 8/1/2004-7/31/2009 

We have studied several aspects of protein kinases, the important proteins which phosphorylate a wide variety of protein substrates and play key roles in signalling. 

• Systematic study of the nature of protein kinase-ligand interactions, based on structural information from the protein databank (PDB) and on static and molecular dynamics (MD) calculations of such structures.

• Protein modeling, which is useful when there are no experimental structures available for a protein or when studying the dynamics and interactions of proteins.

• Protein-protein interactions.

• Detailed study of protein kinase-ligand interactions for particular classes of protein and ligand commencing from PDB or homology model structures, proceeding through docking of ligands, molecular force field static and dynamics calculations and binding free energy estimations.

Publications:

• A Chatterjee; SJ Cutler; RJ Doerksen; IA Khan; JS Williamson “Discovery of novel thienoquinolone derivatives as selective and ATP non-competitive CDK5/p25 inhibitors by structure-based virtual screening,” Bioorganic & Medicinal Chemistry, 22, 6409-6421 (2014). doi: 10.1016/j.bmc.2014.09.043

• G Fu; P. Sivaprakasam; OR Dale; SP Manly; SJ Cutler; RJ Doerksen “Pharmacophore modeling, Ensemble docking, virtual screening, and biological evaluation on glycogen synthase kinase-3β.” Molecular Informatics, 33, 610–626 (2014). doi: 10.1002/minf.201400044

• G Fu; S Liu; X Nan; OR Dale; Z Zhao; Y Chen; DE Wilkins; SP Manly; SJ Cutler; RJ Doerksen “Quantitative structure-activity relationship analysis and a combined ligand-based/structure-based virtual screening study for glycogen synthase kinase-3.” Molecular Informatics, 33, 627–640 (2014). doi: 10.1002/minf.201400045

• RY Patel; RJ Doerksen “Protein kinases-inhibitor database: analysis of structure variability and protein-inhibitor interactions within the P-loop,” Journal of Proteome Research, 9, 4433-4442 (2010). doi: 10.1021/pr100662s; PMID: 20681595 

• J Peng; S Kudrimoti; S Prasanna; S Odde; RJ Doerksen; HK Pennaka; Y-M Choo; KV Rao; BL Tekwani; V Madgula; SI Khan; B Wang; AMS Mayer; MR Jacob; LC Tu; J Gertsch; MT Hamann “Structure activity relationship and mechanism of action studies of manzamine analogues for the control of neuroinflammation and cerebral infections,” Journal of Medicinal Chemistry, 53, 61-76 (2010). doi: 10.1021/jm900672t; PMID: 20017491

• S Prasanna; PR Daga; A Xie; RJ Doerksen “Glycogen synthase kinase-3 inhibition by 3-anilino-4-phenylmaleimides: Insights from 3D-QSAR and docking,” Journal of Computer-Aided Molecular Design, 23, 113-127 (2009). doi: 10.1007/s10822-008-9244-1 PMID: 18839067

Past Funding:

• National Science Foundation. Mississippi EPSCoR Program “Modeling and Simulation of Complex Systems.” NSF EPS 0903787 and NSF EPS 1006883. 8/2009-8/2016. Robert J. Doerksen, Co-Investigator. (PI: Dr. Sandra Harpole, Mississippi State University.)

• National Science Foundation. Mississippi EPSCoR Program. Targeted Seed Grant. “Combined Computational Chemistry and Computational Biology Modeling for Understanding Protein-Protein and Protein-Ligand Interactions.” 1/1/2011-12/31/2011. Robert J. Doerksen, Principal Investigator.

• National Science Foundation. Mississippi EPSCoR Program. Bridge Funding (between programs). “Innovations through Computational Sciences.” EPS-0556308. Robert J. Doerksen, Investigator. (Dr. Sandra Harpole, PI, Mississippi State University.) 8/2009-10/31/2009.

• American Association of Colleges of Pharmacy 2007-2008 New Investigators Program for Pharmacy Faculty. “Rational computer-aided drug design for glycogen synthase kinase-3 inhibition.” Robert J. Doerksen (Principal Investigator). 12/15/2007-6/31/2008.

• University of Mississippi’s National Institutes of Health (NIH) National Center for Research Resources (NCRR) Center of Research Excellence in Natural Products Neuroscience (CORE-NPN) Small Grants Program. “Computational studies on manzamine inhibition of GSK-3beta and CDK5 for treatment of neuroinflammation.” Robert J. Doerksen (PI). 7/1/2007-6/30/2009.

• National Science Foundation. Mississippi EPSCoR Program. “Innovations through Computational Sciences.” EPS-0556308. Robert J. Doerksen, Investigator. (Dr. Sandra Harpole, PI, Mississippi State University). 5/1/2006-4/30/2009.

• National Science Foundation. Mississippi EPSCoR Program. “Innovations through Computational Sciences.” EPS-0556308. Robert J. Doerksen, Investigator. (Dr. Sandra Harpole, PI, Mississippi State University). Education & Outreach funding from 5/2008-8/2009 (administered at U. Mississippi by Dr. Peter Sukanek from Dept. of Chemical Engineering) provided support for several key personnel in the Doerksen research group. 5/1/2006-4/30/2009. 

We are interested to discover new drugs that target a variety of human cancers, including pancreas cancer, liver cancer, and leukemia. 

Publications:

• N Osada; SK Mishra; M Nakano; Y Tokoro; M Nagae; RJ Doerksen; Y Kizuka “Self-regulation of MGAT4A and MGAT4B activity toward glycoproteins through interaction of lectin domain with their own N-glycans,” iScience 27, 111066 (2024). doi: 10.1016/j.isci.2024.111066 

• Y Liu; P Gao; X Liang; Y Zhang; X Yu; X Xue; L Kockaya; P Pandey; RJ Doerksen; X Wang; G Yao; W Chu; X Chen; S Song; MT Hamann; L Li “Prenylated flavonoids with significant anti-hepatoma activity from Daphne giraldii and effects on Fibroblast Growth Factor Receptor 1 (FGFR1),” European Journal of Medicinal Chemistry 247, 115006 (2023). doi: 10.1016/j.ejmech.2022.115006 PMID: 36549116 

• Y Zou; X Wang; J Sims; B Wang; P Pandey; CL Welsh; RP Stone; MA Avery; RJ Doerksen; D Ferreira; C Anklin; FA Valeriote; M Kelly; MT Hamann “Computationally-assisted discovery and assignment of a highly strained and PANC-1 selective alkaloid from Alaska’s deep ocean,” Journal of the American Chemical Society 141, 4338-4344 (2019). doi: 10.1021/jacs.8b11403 PMID: 30758203

• X Wang; J Liu; P Pandey; FR Fronczek; RJ Doerksen; J Chen; X Qi; P Zhang; D Ferreira; FA Valeriote; H Sun; S Li; MT Hamann “Computationally assisted assignment of the kadsuraols, a class of chemopreventive agents for the control of liver cancer,” Organic Letters 20, 5559–5563 (2018). doi: http://10.1021/acs.orglett.8b02207

• J Liu; P Pandey; X Wang; X Qi; J Chen; H Sun; P Zhang; Y Ding; D Ferreira; RJ Doerksen; MT Hamann; S Li “Hepatoprotective dibenzocyclooctadiene and tetrahydrobenzocyclooctabenzofuranone lignans from Kadsura longipedunculata,” Journal of Natural Products 81, 846-857 (2018). doi: http://10.1021/acs.jnatprod.7b00934

• X Wang; J Liu; P Pandey; J Chen; FR Fronczek; S Parnham; X Qi; RJ Doerksen; D Ferreira; H Sun; S Li; MT Hamann “Assignment of the absolute configuration of hepatoprotective highly oxygenated triterpenoids using X-ray, ECD, NMR J-based configurational analysis and HSQC overlay experiments,” BBA (Biochimica et Biophysica Acta) General Subjects, 1861, 3089-3095 (2017). doi: http://10.1016/j.bbagen.2017.09.001 PMID: 28919469

• J Oh; H Liu; HB Park; D Ferreira; G-S Jeong; MT Hamann; RJ Doerksen; MK Na “In silico investigation of lavandulyl flavonoids for the 2 development of potent FAS-inhibitory prototypes,” BBA (Biochimica et Biophysica Acta) General Subjects, 1861, 3180-3188 (2017). doi: 10.1016/j.bbagen.2016.08.001 PMID: 27531709

• CC Chen; M-L Wu; C-T Ho; RJ Doerksen; T-C Huang “Apoptotic induction by andrographolide in HL-60 cells via Ras/ERK/NF-κB and Ras/Akt/NF-κB signaling dependent down-regulation of glyoxalase 1 and HMG-CoA reductase,” Journal of Functional Foods, 14, 226-235 (2015). doi: http://10.1016/j.jff.2015.01.048

• S Prasanna; RJ Doerksen “Topological polar surface area: A useful descriptor in 2D-QSAR,” Current Medicinal Chemistry, 16, 21-41 (2009). doi: 10.2174/092986709787002817 PMID: 19149561

Thanks to several external funding sources and to the University of Mississippi. 

Current Funding:

• National Institutes of Health. National Institute of General Medical Sciences. P20. GM130460. Phase 2. (PI: Dr. Joshua Sharp, Division of Pharmacology). “GlyCORE: Glycoscience Center of Research Excellence.” 9/1/2025-5/31/2030. Doerksen is PI of the Computational Chemistry and Bioinformatics Research Center of Biomedical Research Excellence.

Recent Funding:

• National Institutes of Health. National Institute of General Medical Sciences. P20. GM130460. (Multi-PIs: Dr. Joshua Sharp, Division of Pharmacology and Dr. Samir Ross, National Center for Natural Products Research and Division of Pharmacognosy). “GlyCORE: Glycoscience Center of Research Excellence.” 5/15/2020-3/31/2025; no-cost extension to 8/31/2025. $10,639,190. Doerksen is PI of the Computational Chemistry and Bioinformatics Research Center of Biomedical Research Excellence. 

• National Science Foundation. Research Experience for Undergraduates (REU). “Ole Miss Physical Chemistry Summer Research Program REU.” Third Competitive Renewal. CHE2150352. Robert J. Doerksen, Senior Personnel. (PI: Dr. Nathan Hammer, U. Mississippi.) 9/1/2022-8/31/2025. Doerksen research group will have one summer student each summer. $351,798. 

• National Institutes of Health. National Institute of General Medical Sciences. Supplement to: P20. GM130460. (Multi-PIs: Dr. Joshua Sharp, Division of Pharmacology and Dr. Samir Ross, National Center for Natural Products Research and Division of Pharmacognosy). “GlyCORE: Glycoscience Center of Research Excellence.” 4/1/2023-3/31/2024. $143,467. Sharp is PI and Doerksen is Co-I of this supplement proposal. This was to buy a new GPU cluster for the Computational Chemistry and Bioinformatics Research Center of Biomedical Research Excellence.